학술논문

Improved data analysis for the MinION nanopore sequencer.
Document Type
Article
Source
Nature Methods. Apr2015, Vol. 12 Issue 4, p351-356. 6p.
Subject
*NUCLEOTIDE sequencing
*DATA analysis
*NANOPORES
*SINGLE nucleotide polymorphisms
*SEQUENCE alignment
*DNA copy number variations
*HUMAN chromosomes
Language
ISSN
1548-7091
Abstract
Speed, single-base sensitivity and long read lengths make nanopores a promising technology for high-throughput sequencing. We evaluated and optimized the performance of the MinION nanopore sequencer using M13 genomic DNA and used expectation maximization to obtain robust maximum-likelihood estimates for insertion, deletion and substitution error rates (4.9%, 7.8% and 5.1%, respectively). Over 99% of high-quality 2D MinION reads mapped to the reference at a mean identity of 85%. We present a single-nucleotide-variant detection tool that uses maximum-likelihood parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99%. By pairing our high-confidence alignment strategy with long MinION reads, we resolved the copy number for a cancer-testis gene family (CT47) within an unresolved region of human chromosome Xq24. [ABSTRACT FROM AUTHOR]